The tracks affected are Kids Loop, Tahi, Creek and Grinder.
Event Promotions owner and Moonride race director Murray Fleming said he had changed the event to suit the weather conditions.
"We changed the tracks on the Friday and we also cancelled the 24-hour to minimise the damage," he said.
"It would have been a lot worse if we had ploughed ahead. We have to look at procedures if we get a huge downpour again. We'll be discussing in depth as to whether we change it to a fully road course."
He said the participants had already voted with their feet in terms of what time of year the event should be held. It was to be held in February this year but only 45 teams had entered, leading to it being moved back to its usual May spot. Last weekend more than 250 teams and 50 soloists raced.
Rob Smail, who is the mountain bike club tracks spokesman, said while the trails would be able to be fixed the club would rather not be put in that position.
"Our main concern is it's a problem we shouldn't be dealing with," he said.
"These tracks are going to lose character and it's a character that people love. We're very passionate about it. We need to have discussions to make sure we can avoid this happening again."